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- EMDB-61713: Local refinement of H12 nanotubes assembled from baculovirus caps... -

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Basic information

Entry
Database: EMDB / ID: EMD-61713
TitleLocal refinement of H12 nanotubes assembled from baculovirus capsid protein
Map data
Sample
  • Complex: H12 nanotubes assembled from HaCP
    • Protein or peptide: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
Keywordscapsid protein / self-assembly / Baculovirus / nanotube / VIRAL PROTEIN
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / viral capsid / structural molecule activity
Similarity search - Function
Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme / Viral capsid 39 protein
Similarity search - Component
Biological speciesHelicoverpa armigera nucleopolyhedrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTian K / Rao G / Fu Y / Cao S
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303300 China
CitationJournal: To Be Published
Title: Local refinement of H12 nanotubes assembled from baculovirus capsid protein
Authors: Tian K / Rao G / Fu Y / Cao S
History
DepositionSep 26, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61713.png

Downloads & links

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Map

FileDownload / File: emd_61713.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 512 pix.
= 486.4 Å		0.95 Å/pix.
x 512 pix.
= 486.4 Å		0.95 Å/pix.
x 512 pix.
= 486.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.4928657 - 2.7056937
Average (Standard dev.)0.004192158 (±0.059644535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 486.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61713_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61713_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H12 nanotubes assembled from HaCP

EntireName: H12 nanotubes assembled from HaCP
Components
  • Complex: H12 nanotubes assembled from HaCP
    • Protein or peptide: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein

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Supramolecule #1: H12 nanotubes assembled from HaCP

SupramoleculeName: H12 nanotubes assembled from HaCP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicoverpa armigera nucleopolyhedrovirus

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Macromolecule #1: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39...

MacromoleculeName: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutathione transferase
Source (natural)Organism: Helicoverpa armigera nucleopolyhedrovirus
Molecular weightTheoretical: 60.547168 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM CLDAFPKLVC FKKRIEAIPQ IDKYLKSSKY IAWPLQGWQA TFGGGDHPPK SDLEVLFQGP LGSGGGGGMA LV TVPTATT RLRNFCVFSS VKPLDFCDQY SSPCSSDATV DDGWFVCEYH ASRFFKMEKL ALAIPDGTGN NYYRTVGKSL VDD KAEGIE RILIPSQNNY ETVLNLSLLG PAERLVFYMI YDNKEKQNEI CQQLRMYERF RPEVVEELYN STLRVLALTN PDAY CAQTN TNESRSFGLS VEDDLAFNVL PTFIQNLIRK CVAPESLTIG TEDLQLRNAN TCRITSEGLL ASVRLYNSVQ PKYLY GVNE NRLQIRNVLQ FQGNANALQQ KLSRYELYQI NIPLFLGKQI ISTGR

UniProtKB: Glutathione S-transferase class-mu 26 kDa isozyme, Viral capsid 39 protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1308954
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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